What Might Have Been
by jessid111590
Summary: What might have happened to them if Ian Doyle hadn't walked back in to her life and then taken it away.


**AN: This is my first story posted on here. Thanks to my beta Daisyangel. One shot.**

He sent in his request to be transferred, to get away from everything that reminded him of her; he didn't even do that after Hailey was killed. Hell, even after Hailey died, he said that he would never fall in love again; but he was proven wrong. And now after Emily's death, he had said no more going out. Finally after no word for two months about his transfer, he called Strauss.

"Why the hell have I not been transferred? I put in my request two months ago," He yelled into the phone.

"Agent Hotchner, I never received your transfer request." She said.

"What? How?" he asked.

"I have no idea but your request has never come through onto my desk," she said.

"Thank you, m'am," he said before hanging up the phone.

He goes out in search of the one person who could have removed his transfer from the computer system. As he heads to Penelope's office he sees JJ bringing yet another agent in for an interview.

"Garcia, why the hell did you take my transfer out of the computer system?" he asks.

"Sir, I did it because we cannot afford to lose you. I also did it because the director doesn't want to see this team broken up; he asked me to take it out before anyone else had a chance to see it," she says.

"Fine. I'm taking the rest of today off," he says as he leaves Penelope's office.

JJ flags him down to introduce the new candidate for Prentiss' spot on the team.

"And he is our unit chief, Aaron Hotchner. Hotch, this is Stephanie Smith. She's been working down in counterterrorism for the past 3 years." JJ says.

As he goes to shake her hand, he sees that her smile is like the one that Emily gave to him anytime they were at work; her secret smile.

"Hi, welcome. JJ can finish giving you the rest of the tour. JJ, you know how to reach me if a case comes in." he says before going to his office to get his things.

In JJ's office

"You wanted to see that he still cares about you, Emily. Penelope told me almost two months ago that he had requested a transfer but the director had her take it out before anyone could see it. You may not have seen it just now but we've been the ones he's been taking his pain out on. When he gets mad, you'd better stay out of his way. He even has yelled at Rossi for little things. There are times when I walk past his office and he's just staring out into the bull pen, looking at your desk. Hell, he even leaves early; even when he has files of paperwork he should be doing sitting on his desk," JJ says looking at her friend. "I don't care if you believe me but he refuses to come out to the bar to distress with us after a case. He's totally lost without you here. You have always been his rock, especially after Hailey died. The last six months have been really hard on him."

"What's going to happen when I come back to the team though?" Emily asks.

"We are going to have to keep you as Stephanie for a few days to transition you back in. After that we should be home free to making you look like yourself. I have no idea how this is going to affect him though. You are going to have to tell him yourself because he is already going to be pissed off at me for not telling him two months ago that you were still alive." JJ says.

"I can handle being Stephanie for a few days, no more than a week tops, but I need to come back as myself as soon as possible not just for him but also for myself," Emily says as they walk out of JJ's office.

"Welcome to the team. How about I give you the grand tour?" JJ says with the team looking on.

"Sure," Emily says.

"Hey, guys this is Stephanie Smith. She's our new agent. This will be your desk. Stephanie this is Derek Morgan, Spencer Reid and Dave Rossi. Penelope Garcia works down there and you saw both mine and Hotch's office earlier," JJ says pointing to Emily's old desk. "She was working in counterterrorism and has decided to join us up here at the big leagues. Well I'll let you get settled in and if you need anything just ask."

"JJ wait where did Hotch go to?" Derek asks.

"No clue. The last thing that I heard him says was that he was taking the rest of the day off," she says before walking back to her office.

In Hotch's Car

He couldn't believe that JJ would bring someone who looked exactly like Emily into the office. The small smile that graced Stephanie's lips was almost identical to the one that Emily had given him at work. He managed to get home before, as soon as he got into the driveway, the memories came flooding back. The one that always seemed to appear was the last night they spent together.

_Flashback_

_It was three o'clock in the afternoon and he had left work early to spend some time with Jack. They had gone grocery shopping and had even spent some time out in the backyard playing soccer. He was surprised to hear a car pulling into his driveway but once he saw that it was Emily, he knew that something was going on with her. She rarely came over before Jack was in bed. As he walked out of the house to greet her he asked, "Did a case come up?"_

"_No. I just thought that I would come by early tonight," she said as she wrapped her arms around his waist. "So where's Jack?"_

"_He's out back working on some soccer moves," He says as they move into the kitchen. "Want to help me get dinner ready?"_

"_Is it ok if I go out and play around with Jack for a bit first?" she asks._

"_Sure," he says._

_It was really unusual for Emily to want to play with Jack. That was why she would normally only come over after he was in bed. But at the time, he was glad to see that she was taking an interest in Jack; maybe in a couple weeks he could ask her to move in with them. She and Jack seemed to hit it off. They talked all throughout dinner about topics they were interested in. He had never heard her speak about any of the topics she was talking to Jack about._

_She had even ask him if she could put Jack to bed that night and Jack even let her read him a story. As she climbed in bed next to him, she just cuddled up along his side before stretching up to kiss him. He should have realized then what was happening. She never liked to cuddle before sex and most certainly didn't like to cuddle after sex. He couldn't even get her to spend the night. So after they had sex, he was surprised when she curled up next to him instead of leaving the bed._

"_Em, move in with Jack and I." he says._

"_Maybe," she says as she starts to fall asleep. The thought running in her mind was that after Doyle was dead, she'd have a place to call home and a family around her._

_When he woke up the next morning, he realized that what he felt a few hours ago wasn't a dream. Emily wasn't in his bed or even his house._

_It wasn't until later on at work that he realized she had left. He figured that out when he called her cell and it went off in her desk with her gun and badge. When Morgan found her bleeding to death on the floor of that warehouse and JJ came out after talking to the doctor, he knew she wasn't coming back._

As he sat in his car remembering, he realized, yet again, that there were so many signs that night that he should have realized something was up.

Emily knew exactly where he was headed so she headed there too. As she sees him sitting in the car, she also is remembering the memories. The one thought running through her mind was "Now that Doyle's dead, I cannot even go back to the one place that I was willing to call my home. I cannot even tell my family that I am back yet." As she sits in her car, she wonders what his reaction is going to be when she tells him it's her. What he's going to say when she tells him that she had to have an abortion because the doctors had said that all the stress was going to be a hazard for both her and their baby? No one else knew about that yet because it was still too painful for her to talk about.

As he was getting out of the car, he noticed the new girl sitting outside his house in her car. As she realizes that he's seen her car, she turns the car on to drive away but something about him stops her. But as he starts walking towards her, she knows she needs to get out of there. As she heads to her place, she doesn't even try to stop the tears from falling. As she pulls into the driveway of her rental apartment, she sees that JJ is there to watch movies since they had schedule a movie night a few days prior.

"JJ, is there any way we could do movie night tomorrow?" she asks.

"Why? What's up?" JJ asks.

"I just want to get settled in, take a bath, and get some sleep tonight. I'm sorry it has just been a really long day." She says.

"Ok. See you at the office tomorrow then." JJ says getting back into her car.

"Thanks. See you tomorrow." She says as she opens the door to her apartment.

As she walks into the apartment, the tears start to fall again and like before there is no stopping them. She gets something small to eat, takes a bath and is asleep before 9:00 p.m. For the first time in months, she actually gets a good sleep without the nightmares of Doyle.

As her alarms goes off the next morning, she is dreading to go into work because of Hotch catching her sitting outside his house. She really didn't want to have to be Stephanie Smith any longer; she wanted to be able to stop hiding who she was and what she wanted for herself. She puts on one of her suits that makes her feel like her old self but she can't wear her hair like she used to because of the extensions that had to be put in. She grabs the book with the picture of the baby in it just in case she needs something to do.

As she walks into the bull pen she sees that she is the first one there. She looks up and sees that Hotch is in his office working on paperwork. She sits down and starts on the final transition to the team paperwork. When JJ comes in, she hands Emily a note saying that the first thing that she can do is get the extensions taken out and her hair cut to normal length.

"Thank God. I can't wait to be back to my old self." Emily says as her cell phone rings.

"Old self? What's your old self?" Derek asks coming in at the end of that conversation.

"Got to take this. Be back in a second." She says. "Hey, mom."

"All I get is a hi mom. You've been gone six months and no one, not even your team, knew where you were at." Mrs. Prentiss says.

"I couldn't let them know where I was at. I told you that," Emily says. "You have no idea how much I wanted people to know but it was a safety risk. Hell, me sending you that letter was a really big safety risk but I had to take it."

"Since your back in town, how about we go out to lunch today, Em? Please. I want to make sure you are ok," Mrs. Prentiss says. "Have you told the father about the baby, yet?

"Fine. I think that I can do that," she says. "No, I can't just yet and no I will not invite him to lunch with us."

"Will you at least tell me who the father is?" Mrs. Prentiss asks.

"No, I will not. I will meet you down at the deli on 23rd for lunch. Now I have to get back to work. I will see you later." She says before she hangs up the phone.

When she turns around she finds Hotch looking at her, she turns and runs to the nearest bathroom.

"I'll go get her. I think she's worried about messing something up," JJ says.

"Fine, bring her to the conference room after you get her," Hotch says.

"Em, what is going on?" JJ asks.

"Did you just say Em, JJ?" Penelope asks as she comes out of a stall.

"Yea she did, Pen. It's me," Emily says. "I'm back or I will be back, as myself, next week."

"Pen, she will explain more to you later on, since she has transition paperwork to still get done and can't come on this case, but all three of us are needed in the conference room right now." JJ says. "Are you ok to go, Em?"

"Yea I'm fine. Let's just get this over with," she says as they walk to the conference room.

"Everything ok?" Hotch asks.

"Fine." she says without looking at him.

"Ok. Agent Smith, you will be staying here to help Penelope," Hotch says.

"Sure," she says as she follows Penelope out to her office.

"JJ, is everything ok with Agent Smith?" Hotch asks.

"I don't know. You know we understand that your still beating yourself up about Emily but you really need to embrace the new girl and then maybe you'd find yourself opening up, not just to her but to the entire team. I'm sick of people not realizing things until the last minute," JJ says as she walks toward her office.

"She's right, Aaron. Ever since Emily died, you refuse to come out with us and when we are all here, you lock yourself in your office until you decide it's time for you to leave," Rossi says as he heads to his office.

In Penelope's office

"I can't believe your back. JJ told me a while back that you weren't gone but I didn't believe her. God, it's so good to have you back. So tell me why you have to wait a week before coming back as yourself. And I take it Hotch has no clue yet," Pen says.

"It's a precaution just in case Doyle had people follow me. Tonight I'm getting the extensions out and getting my hair cut to its normal length. The rest of the week is about changing back to me. I am happy that the team is on a case though. I now get to change my appearance without people watching me. No, Hotch has no idea and he cannot know until he gets back from this case when he sees my transition papers on his desk. I have to go get something from my desk," Emily says.

She comes back with the book and the rest of her transition papers. Penelope grabs the book from her hand and opens it but when she sees what Emily is using as the bookmark, she closes the book and looks at Emily. She sees the tears about to fall from Emily's eyes as she looks at the picture.

"Em, does Hotch know?" Penelope asks.

"No. No one knows about anything that happened or the fact that I was forced to give up our child because they said the stress was going to kill either or both of us," Emily says as she turns away from Penelope. "No one would understand how hard it was for me to say yes. I wanted to keep her."

"Hun, come here," Penelope says as she turns Emily around to give her a hug. "Shit. Let me answer this. Goddess of All Knowing, what can I help you with?"

"Hey, Baby Girl, ready to work some magic?" Derek asks.

"Sure give me a second to get back to my computers," Penelope says. "Ok go ahead."

Emily just sits there working on her paperwork. She hears Penelope switch off speaker phone and she figures who Penelope was talking to; it had to be Hotch checking to make sure Agent Smith was there still. She wanted to take the phone out of Penelope's hand and scream, "Of course I'm still here." Sensing that Penelope turned to where Emily couldn't reach the phone. Emily just laughed at the fact that her friend knew exactly what she was thinking about doing and then she turns back to her paperwork.

"Hey, Pen, want to go to lunch with me and my mom?" she asks. "One thing though, my mom is going to ask me who the baby's father is. She doesn't know that I was involved with Hotch and I really don't want her to know that he was the father just yet."

"Sure, let me just get a tech to cover for me." Pen says. "Oh. Ok."

At the Deli

"Mom, this is Penelope a very important member of my team," Emily says. "And yes, she knows about everything."

"Ambassador Prentiss." Penelope says shaking the ambassador's hand.

"Since my daughter said that you know everything, then would you care to divulge who the father of the baby was?" Mrs. Prentiss asks.

"Actually that's one thing that she didn't tell me," Penelope says.

"I guess I'm just going to have to guess. Let me see. I think that it was that handsome black man on your team, Derek Morgan." Mrs. Prentiss says.

"Actually, I know that one to be false seeing as Derek and I are married," Penelope says.

"Pen, you never told me that," Emily says. "Congratulations."

"Thanks. It has to do with you though. When the team lost you, Derek finally wised up and proposed," Penelope says as her cell phone rings. "Sorry I have to take this."

"Hey Goddess, why is there another tech in your seat?" Derek asks.

"I'm out to lunch with Stephanie. We'll be back in about a half an hour though." She says. "Was she able to get you the information that you needed?"

"Yea. I just wanted to make sure everything was ok with you." he says.

"I'll call you when we get back to the office," she says before hanging up. "Sorry it was a work call."

"Do you need to get back to the office?" Emily asks.

"No, some people just forget that I too need to eat," Penelope says.

After exhausting more questions about the baby's father, the three women decide it's time to get back to work. Every time the team calls Penelope is asked if agent Smith was still there.

"You know every time he calls I just want to take the phone from you and scream 'of course I'm still here'," Emily says.

"Well the other agents that came into take your spot, left before finishing the rest of their transition paperwork," Penelope says. "And Hotch thinks you're just some newbie named Stephanie Smith. He doesn't know it's you."

"Ok, I guess I can understand that. Hey I have to get going. Finally heading to try and get a piece of my old self back. I'll see you tomorrow," Emily says heading out of Penelope's office to go back to her desk to get her things.

After a week spent on transition paperwork, Emily was starting to get sick of sitting in the office constantly. So when she came in and saw the note from Penelope saying the team was headed home, Emily put her transition paperwork in the shelf on Hotch's door, with a little note telling him where she would be, and headed to the one place she was willing to call home.

As Hotch arrived at his office door he read the paperwork that was left in the shelf. When he got to the parts, that agent Smith was to fill out, he saw the one name he hadn't expected to see again; Emily Prentiss. He goes over to JJ's office to ask if this paperwork was real and why wasn't he told that agent Smith was actually Emily.

"JJ is this paperwork real?" he asks.

"Give it to me to look at. Yep very real," JJ says.

"Then why the hell wasn't I notified that Emily, or as you told me Stephanie, was alive and coming back to our team?" he asks.

"Hotch, I was the only person who knew that she was alive, from this team. It was a safety precaution and a major risk for me to know. I told you that because that was the name she had been under. She gave me a week to get everything ready for her to come back to this team as herself," JJ says. "Looks like there is a note for you back here and you might want to read it."

The note said:

_**Hey A,**_

_**You remember the last question you asked me? If so, then you know exactly where to find me and yes I still have my key.**_

_**EP**_

"Looks like my paperwork is just going to have to wait. Thanks, JJ," Hotch says before leaving. "Everyone, take the rest of today off and don't worry about the paperwork."

"What is going on with him?" Derek asks.

"He just found out that someone he never thought he would see again is back," Rossi says after grabbing his jacket.

"Who?" Reid asks.

"Emily Prentiss." Garcia says. "Ready to head home, hot stuff?"

"Seriously, Prentiss is back?" Reid asks.

"Yes she is, Spence." JJ says as she heads out to the elevators.

At Hotch's house

"God, I have missed this place so much," Emily says as she sets her stuff on the floor in the hallway.

As she sat down on the couch, she grabbed the picture of their daughter and just held on to it. She had yet to figure out a way to tell him about her.

As he walks into the house, he sees her sitting on the couch, with her eyes closed, holding on to a picture. He also saw the tears falling freely from her closed eyes. He looked at the photo and saw the name Abigail Elizabeth Hotchner. His breath caught in his throat and one thought ran through his head. She's pregnant with my child but she doesn't look pregnant.

Emily didn't realize anyone was in the house, let alone the living room with her, until Hotch sat down next to her and pulled her to him. As she looked up at him, she saw the look of relief, to see her, on his face.

"God, Em, you have no idea how happy I am right now. I've missed you so much," he says as he leans into kiss her.

"Aaron, we really need to talk." She says. "It's about this picture."

"Ok," he says.

"I found out two weeks after I had left that I was pregnant and actually managed to make it to 4 months with only taking prenatal vitamins. But I collapsed one day at work and witness protection found out that I was pregnant and that the stress of where I was and that I had no one around to help me, they told me I had a choice to make: either I come back here and worry about Doyle finding and killing everyone or give up the baby." She says before taking a breath. "The doctor agreed. Everyone kept saying that the stress was going to kill either or both of us, if I didn't give her up. I knew what they were saying was true but I wanted to keep her. So the next time that I collapsed, I knew that I had to give her up or else neither of us would make it. You have no idea how hard it was for me to not even get a chance to tell you or Jack."

"Hey, it's ok, Em we can try again." He says, amazed that she had let him in on something that had upset her while she was away. "Hey, don't cry. I'm not mad at you. I want to try again that way I can see you pregnant with our child."

"You're not mad?" she asks.

"Nope. I'm just glad to have you back here with me," he says. "Let me call Hailey's parents and see if they are willing to watch Jack for another night. Then we can go and try to make another baby," he says with a devious smile.

After a night of being thoroughly being loved by Aaron, she lies in bed with a smile on her face and watches him as he tries to sleep.

"Did you think about moving in with us while you were away?" he asks.

"All the time. You have no idea what it took for me to stay away that day you caught me outside here since I was Stephanie Smith and not Emily Prentiss. I wanted so bad to just walk in with all my things," she says before kissing his neck.

"Why did you have to come back as Stephanie Smith?" he asks as he pulls her even closer to him.

"I had to because they were still trying to rundown all the partners of Doyle to make sure that no one had ever heard of the name Emily Prentiss," she says.

Six months later

As the team gathers to celebrate Jack's birthday, they get to also meet the newest member to the team; Derek and Penelope's daughter, Chole.

"I still cannot believe that you didn't tell me, when you found out it was me, that you were pregnant," Emily says.

"Yea, well we could say the same thing to you too, miss," Penelope says.

"Well we didn't find out about you until just before you had her. At least with me you can see, two months in, that I am pregnant." Emily says as she grabs the cake.

"Yea well it's easier to hide one baby under clothes not two. Plus you know he likes to see you pregnant and glowing every day." Penelope says looking over at Hotch and Rossi working the grill.

"That he does." Emily says. "Hey, hun, when is the food going to be done?"

"In a couple minutes. Why?" Hotch says.

"Well it looks like Jack is hungry and you know me and these two." She says as the front door bell rings. "Someone's at the front door."

As she opens the front door, she sees that her mother and father were here to celebrate with them. Little did she know, Aaron had a surprise for her and had made sure that her parents were going to come and celebrate with them.

"Mom, Dad. You've met Aaron before. And well this is the rest of our team." Emily says while walking them out to the backyard. "This is Dave Rossi, Penelope, Derek, and Chole Morgan, JJ, and Spencer Reid."

"Hey, nice to see you again, Mr. and Mrs. Prentiss. Go have a seat the food will be ready shortly." Hotch says. "Go sit and talk. I'll finish bringing everything out."

After dinner it was time for presents. Jack opened all of his and then he and Hotch both had a surprise for Emily. As Jack slipped his arm into hers, she turned to see Hotch getting down onto one knee.

"Emily, we and everyone here can see that we've had a bad year. But when you came home to the both of us everything started to get better. Now will you do me the honor of becoming my wife and do Jack the honor of becoming his mother?" Hotch says opening the box and showing her the ring that he had had designed by the book she had left before she left.

"Yes to both of you." She says crying.


End file.
